Publication

Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq

NVR Mutha, WK Mohammed, N Krasnogor, GYA Tan, WY Wee, Y Li,

Scientific reports 9 (1), 7664

Streptococcus gordonii Challisin protease is required for sensing cell--cell contact with Actinomyces oris

WK Mohammed, N Krasnogor, NS Jakubovics

FEMS microbiology ecology 94 (5), fiy043

Isolation of Lactobacillus salivarius from children and purification of bacteriocin to inhibition cancer cell in vitro

WKM Al-Tememy, IA Al-Ani, MQ Al-Ani, NT Al-Alusi, S Ismail

International Journal on Advanced Science, Engineering and Information

Transcriptional responses of Streptococcus gordonii and Fusobacterium nucleatum to coaggregation

NVR Mutha, WK Mohammed, N Krasnogor, GYA Tan, SW Choo, ...

Molecular oral microbiology 33 (6), 450-464

Simbiotics: A multiscale integrative platform for 3D modeling of bacterial populations

J Naylor, H Fellermann, Y Ding, WK Mohammed, NS Jakubovics, ...

ACS synthetic biology 6 (7), 1194-1210.

Molecular genetic study of Pseudomonas aeruginosa  DNA repair system 

 Waleed Khalid Mohammed. Journal of university of Anbar for Pure science: : Vol.7:NO.1: 2013.

Comparison and Detection of Helicobacter pylori in Stool Specimens by use Polymerase Chain Reaction technique and immunochromatographic assay

Waleed Khalid Mohammed. Al-Anbar J. Vet. Sci., Vol.: 9 No. (2), 2016 ISSN: 1999-6527

Lectures

General introduction

WHAT IS BIOLOGY?

The science which deals with the study of living objects and their life processes is called biology (Greek words, bios – life, logos – study). It covers all aspect of the study of living creatures like occurrence, classification, ecology, economic importance, external form, organization, internal structure, nutrition, health and other.

Branches of Biology: 

There are three major branches of biology – botany, zoology and microbiology. Botany is the branch of biology which deals with the study of different aspects of plants.

Zoology is the branch of biology connected with the study of different aspects of animals. Aristotle is known as the father of Zoology. 

 Microbiology is the branch of biology dealing with the study of different aspects of microorganism. Leeuwenhoek is known as the father of Microbiology.

MAIN BRANCHES OF BIOLOGY

Some of the main branches of biology are briefly discussed below:

1.  Taxonomy: It is the science of identification, nomenclature and classification of organisms.
2.  Morphology: It is the study of external form, size, shape, colour, structure and relative position of various living organ of living beings.
3.  Anatomy: It is the study of internal structure which can be observed with unaided eye after dissection.
4.  Histology: It is the study of tissue organization and structure as observed through light microscope.
5.  Cytology: It is the study of form and structure of cells including the behaviour of nucleus and other organelles
6.  Cell Biology: It is the study of morphological, organizational, biochemical, physiological, genetic, developmental, pathological and evolutionary aspects of cell and its components.
7.  Molecular Biology: It is the study of the nature, physicochemical organization, synthesis working and interaction of biomolecules that bring about and control various activities of the protoplasm.
8.  Physiology: It is the study of different types of body functions and processes.
9.  Embryology: It is the study of fertilization, growth, division and differentiation of the zygote into embryo or early development of living beings before the attainment of structure and size of the offspring.
10.  Ecology: It is the study of living organisms is relation to other organism and their environment.
11.  Genetics: It is the study of inheritance of characters or heredity and variations. Heredity is the study of expression and transmission of traits from parents to offspring.
12.  Evolution: It studies the origin of life as well as new types of organism from the previous ones by modifications involving genetic changes and adaptations.
13.  Virology: It is the study of viruses in all their aspects.

http://www.iasplanner.com/civilservices/ias-pre/general-science/main-branches-of-biology-and-fields-of-biology

General characteristics of living things

When examining the characteristics of organisms, there are two basic categories of organisms- living and non-living. There are several characteristics that exist to classify an organism as a living thing. Living organisms must be made of cells, reproduce, use energy, grow and develop, respond to stimuli, adapt to their environment, and maintain homeostasis. Non-living organisms, then, lack one or more of these characteristics. For example, plants and animals are living while rocks and cars are not living. It is important to understand the basic characteristics of organisms because these features determine how scientists classify, study and discuss all matter. Because of this information, all living matter can be classified in a complex taxonomy system that shaped the way organisms are named and studied.

These are the three characteristics of living organisms.

1. Living things are organized
2. Living things obtain and use energy
3. Living things Maintain Homeostasis.
4. Reproduction.
5. Living things adaptations

1- Living things are organized: - The levels of organization began with atoms which are the basic units of matters, atoms combine with other atoms of the same or different elements to form molecules. The cell composed of variety of molecules working to gather, organism may be Unicellular, paramecia _ Multicellular, human. Many living things that are unicellular – they consist of a single cell. Other living things are multicellular, consisting of many cells – many trillions of cells in the case of human adult. The cell is in several senses the basic unit of a living organism. There are more than 200 distinct kinds of cells in the human body. All living things are composed of cells, and all cells arise from pre-existing cells

 Similar cells combine to form tissue (nerve tissue), tissue make up organs (brain), organs work to gather in system (brain work with spinal cord and a network of nerves to form nervous system). Organ systems are joined to gather to form a complete living organism such as a human.

2- Living things obtain and use energy: - Cells cannot survive on their own. They need power to stay alive. They need energy to perform functions such as growth, maintaining balance, repair, reproduction, movement and defence. This means all living organisms must obtain and use energy to live.

Energy is the power to do things. This power comes in many ways and forms, but they can all be linked to the sun. It is the source of all energy.

The process of obtaining and using energy by living organisms are best explained by three important scientific terms namely Anabolism, Catabolism and Metabolism.

.  

5. Anabolism (constructive anabolism)

This is a process whereby living organisms use simpler substances to put together, or build complex substances such as carbohydrates, proteins and fats for storage. Such an activity is known as an anabolic activity. Nutrition is anabolism process as it helps in the building up of the body tissue.

A living organism can either make its own food or depend on others to make food for them. For example, green plants produce their own food from a process called photosynthesis. They use the chloroplasts in their cells to capture energy in sunlight. They combine it with water and carbon dioxide from the air to produce sugars for themselves. Other organisms take diffusible and non- diffusible complex organic substance as food (ingestion) in animals. The non-diffusible foods substance is converted into diffusible forms (digestion). The digestion food is absorbed and distributed in to various parts of the body and is ultimately converted into protoplasm (assimilation). The undigested waste matter is passed out of the body as feces (egestion) or defecation

5. Catabolism (destructive catabolism)

This is when the cells in living organisms, breakdown complex substances and molecules into simpler substances, often to release energy for use.

5. Respiration

a catabolism process as it tends to destroy the tissue substances by oxidation. It involves intake the oxygen and outgo of carbon dioxide. Oxygen oxidizes the tissue substances, CO2 and water are produced and energy is liberated. This energy is utilized for performance of various bodily functions.

5. Metabolism
   This is the sum of all the chemical reactions (anabolic and catabolic activities) that go on in the cells of living organisms. It is a continuous process because the moment metabolism stops, the living organism will die.

3-Living things Maintain Homeostasis :-To survive it is imperative that an organism maintain a stat of biological balance or homeostasis ,temperature , moisture level, acidity or other physiological factors must remain within the tolerance range of the organism .Homeostasis is maintained by systems that monitor internal conditions  and make routine and necessary adjustments .

Examples of homeostasis include the regulation of body temperature, the pH of extracellular fluid, or the concentrations of sodium, potassium and calcium ions. Muscular activity generates heat as a waste product .This heat is removed from our bodies by sweating .

pH :- In human pH need to be maintained within a narrow range .The pH of blood is 7.4  that is slightly basic (alkaline ) .If the blood pH drops to about 7 acidosis results .If the blood pH rises to about 7.8 alkalosis results .Both conditions can be life threatening , so the blood must be kept around 7.4 .

Carbonic acid is a weak acid that minimally dissociate and then re-forms in the following manner :

 H2CO3             ------dissociates-----------   H+      +       HCO3-

Carbonic acid    ------re-forms------               Bicarbonate ion

Blood always contains a combination of some carbonic acid and some bicarbonate ion. When hydrogen ion H+ are added to blood the following reaction reduces acidity

H+     +    HCO3-  --------------------   H2CO3

When hydroxide ions OH- are added to blood ,this reaction reduces basicity .

OH-      +    H2CO3  ----------------------- HCO3- + H2O

These reactions prevent any significant changes in blood pH.

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4-Reproduction: - is the process through which new organisms, or offspring, are produced by a parent organism.

 Asexual reproduction (fission ,budding and fragmentation ) involves one parent organism and produces an identical offspring. Bacteria reproduce asexually as well as some animals such as starfish that use asexual reproduction to regenerate limbs.

 Sexual reproduction involves two parent organisms and produces a genetic combination of the two. In sexual reproduction, the offspring has a unique genetic code because of the variety of combinations that could occur from parents. Most living organism use the chemical DNA (deoxyribonucleic acid ) as the physical carrier of inheritance and the genetic information .Some organisms such as retrovirus ( of which HIV is a member ) use RNA (ribonucleic acid ) as the carrier .

5-Living things adaptations:- adaptations are modification that make organism better able to function in a particular environment , penguins are adapted to an aquatic existence in the Antarctic . An extra layer of downy feathers is covered by short , thick feathers that form a waterproof coat ,feet and tails serves as rudders in the water .flat feet also allow them to walk on land . a polar bear has very thick fur to trap their body heat in the cold artic temperatures

6- Living things respond: - In order to survive, living things must respond to stimuli in their environment. This responsiveness is active and requires a set of systems to detect a change and respond to it. Living things change according the light, temperature, and chemicals in their environment. An example of this would be a person touching a hot stove and immediately pulling their hand away.

7- Excretion: - All living things excrete. As a result of the many chemical reactions occurring in cells, they have to get rid of waste products which might poison the cells. Excretion is defined as the removal of toxic materials, the waste products of metabolism and substances in excess from the body of an organism.

8- Secretion:- The living things produce many useful substances such as enzymes ,hormones….etc. These substances are produced in different parts of body and are sent to other parts.

9- Growth and development: -. Growth can be the adding of cells to an organism to cause it to change in size or mass. This can also be exhibited in the change of appearance or form. For example, tadpoles develop into frogs with the addition of cells and the change of appearance.     

10- Movement or motility: - Most of the animals move bodily from one place to another with the help of certain organs or organelles, this called locomotion.

11-Interactions: - living things interact with their environment as well as each other. Organisms obtain raw materials and energy from the environment or another organism. The various types of symbioses (organismal interactions with each other ) are examples of this interaction .

Symbiosis: - An interaction between two or more species living together, may be parasitic, commensal or mutualism, The relationship between two organism .

12-Death: - Living things ultimately suffer from death.

The Structure of Prokaryote and Eukaryote Cells

Prokaryotes are simple, small cells, whereas eukaryotic cells are complex, large structured and are present in trillions which can be single celled or multicellular. Prokaryotic cells do not have a well-defined nucleus, but DNA molecule is in the cell, termed as nucleoid, whereas eukaryotic cells have a well-defined nucleus, where genetic material is stored. Based on the structure and functions, cells are broadly classified as Prokaryotic cell and Eukaryotic cell

Prokaryotic Cells are the most primitive kind of cells and lack few features as compared to the eukaryotic cell. Eukaryotic cells have evolved from prokaryotic cells only but contain different types of organelles like Endoplasmic reticulum, Golgi body, Mitochondria etc, which are specific in their functions. But features like growth, response, and most importantly giving birth to the young ones are the commonly shared by all living organisms.

Classification of Living Organisms the Taxonomic System

 Domain is the largest classifying system. There are three domains that contain all the known living organisms on the planet.

 I-The domain Eukarya contains plants, animals, fungi, and protists.

II-The domain Bacteria contains cyanobacteria and heterotrophic bacteria.

III- The l domain, Archaea, contains halophiles and thermophiles, which are not bacteria.

 Archaea are organisms that survive in the most extreme environments on the planet such as thermal vents that reach over 100 degrees Celsius

There are four Kingdoms: Protista, Fungi, Plantae, and Animalia.

Kingdom Protista: - contains protists that are usually single-celled organisms such as algae.

 Kingdom Fungi:- contains decomposers such as fungi, yeast, and mold.

Kingdom Plants:- that have chlorophyll, cell walls and vacuoles can be classified in Kingdom Plantae.

 Kingdom Animalia:- contains any animal that survives by eating other organisms. Animals cannot produce their own food, therefore they rely on other plants and animals to serve as their food source. From there each Kingdom is broken down further into Phylum, Class, Order, Family, Genus, and Species.

Binomial nomenclature. This format uses the Genus and Species to give animals their distinct scientific name. For example, human would be the familiar name while Homo sapiens is the scientific name.

 Kingdom:   Animalia 
     Phylum:   Chordata
          Subphylum:   Vertebrata
             Class:   Mammalia  

                Order:   Primates
                                   Suborder:  Anthropoidea
                                        Superfamily:  Hominoidea
                                             Family:   Hominidae
                                              &a

No.	Subjects	Lectures	Stage	File	Video
1	biology	Cell structure and function	First
2	biology	The Biomolecules of Cells	First
3	biology	Structure and function of Cytoplasm	First
4	biology	Medical Biology	First
5	biology	Introduction to molecular biology	First
6	biology	( BASIC BACTERIOLOGY	First
7	biology	Introduction to Viruses	First
8	biology	Immunity	First

Other

• Experience

• lecturer of Microbiology and immunology (2013-2018), Department of Basic science, College of Dentistry, University Of Anbar, Iraq.
• Assistant lecturer of Microbiology and immunology (2011-2013), Department of Basic science, College of Dentistry, University Of Anbar, Iraq.
• Director of research and training development of medical lab trainees and postgraduate (2011-2013).
• Researcher in Medical Microbiology and Molecular Biology Department of Basic science 
• Major interest is in Molecular Biology and Bacteriology
• Good experience in recombinant DNA and Cloning techniques, cDNA library construction and PCR methodology, RT-qPCR, Northern Analysis, RNA extraction and RNAseq.